Multiple sequence alignment - TraesCS5D01G305400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G305400 chr5D 100.000 2696 0 0 1 2696 400292478 400295173 0.000000e+00 4979.0
1 TraesCS5D01G305400 chr5A 93.097 1130 52 8 266 1378 505623250 505624370 0.000000e+00 1631.0
2 TraesCS5D01G305400 chr5A 94.301 386 21 1 1371 1756 505624424 505624808 8.310000e-165 590.0
3 TraesCS5D01G305400 chr5A 85.791 556 30 19 2031 2555 505625178 505625715 6.560000e-151 544.0
4 TraesCS5D01G305400 chr5A 89.381 226 16 6 1829 2046 505624939 505625164 7.350000e-71 278.0
5 TraesCS5D01G305400 chr5A 90.123 162 14 2 106 265 505622972 505623133 2.720000e-50 209.0
6 TraesCS5D01G305400 chr5A 92.958 142 8 1 2557 2696 505625774 505625915 3.520000e-49 206.0
7 TraesCS5D01G305400 chr5A 84.615 104 8 4 1 104 696850729 696850634 2.210000e-16 97.1
8 TraesCS5D01G305400 chr5A 84.615 104 8 4 1 104 696889835 696889740 2.210000e-16 97.1
9 TraesCS5D01G305400 chr5B 92.342 1123 52 11 265 1378 480297909 480299006 0.000000e+00 1567.0
10 TraesCS5D01G305400 chr5B 89.514 658 28 13 1763 2380 480299472 480300128 0.000000e+00 795.0
11 TraesCS5D01G305400 chr5B 91.816 391 23 3 1371 1760 480299056 480299438 1.100000e-148 536.0
12 TraesCS5D01G305400 chr5B 90.062 161 11 3 106 265 480297643 480297799 1.270000e-48 204.0
13 TraesCS5D01G305400 chr5B 88.591 149 9 3 2400 2547 480301145 480301286 9.920000e-40 174.0
14 TraesCS5D01G305400 chr1B 84.068 885 77 27 534 1378 645520610 645519750 0.000000e+00 795.0
15 TraesCS5D01G305400 chr1A 80.638 909 95 40 534 1378 560313559 560314450 1.760000e-176 628.0
16 TraesCS5D01G305400 chr1A 82.188 393 43 12 1371 1760 560314518 560314886 2.020000e-81 313.0
17 TraesCS5D01G305400 chr1D 85.526 532 47 15 870 1378 467626590 467626066 1.840000e-146 529.0
18 TraesCS5D01G305400 chr1D 83.929 336 25 5 534 863 467627652 467627340 7.300000e-76 294.0
19 TraesCS5D01G305400 chr4D 83.966 237 31 5 1524 1760 432433841 432434070 1.260000e-53 220.0
20 TraesCS5D01G305400 chr4D 84.444 90 10 4 17 104 85729539 85729626 4.780000e-13 86.1
21 TraesCS5D01G305400 chr7D 97.059 102 3 0 1 102 610783160 610783261 3.570000e-39 172.0
22 TraesCS5D01G305400 chr3A 93.333 105 6 1 1 104 71122566 71122462 1.290000e-33 154.0
23 TraesCS5D01G305400 chr3D 91.346 104 9 0 1 104 69790556 69790453 2.800000e-30 143.0
24 TraesCS5D01G305400 chr4B 90.476 105 7 2 1 104 91158191 91158293 4.680000e-28 135.0
25 TraesCS5D01G305400 chr4B 82.653 98 12 4 12 105 256338827 256338731 6.190000e-12 82.4
26 TraesCS5D01G305400 chr7B 82.979 94 10 5 16 105 458788345 458788254 2.230000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G305400 chr5D 400292478 400295173 2695 False 4979.000000 4979 100.000000 1 2696 1 chr5D.!!$F1 2695
1 TraesCS5D01G305400 chr5A 505622972 505625915 2943 False 576.333333 1631 90.941833 106 2696 6 chr5A.!!$F1 2590
2 TraesCS5D01G305400 chr5B 480297643 480301286 3643 False 655.200000 1567 90.465000 106 2547 5 chr5B.!!$F1 2441
3 TraesCS5D01G305400 chr1B 645519750 645520610 860 True 795.000000 795 84.068000 534 1378 1 chr1B.!!$R1 844
4 TraesCS5D01G305400 chr1A 560313559 560314886 1327 False 470.500000 628 81.413000 534 1760 2 chr1A.!!$F1 1226
5 TraesCS5D01G305400 chr1D 467626066 467627652 1586 True 411.500000 529 84.727500 534 1378 2 chr1D.!!$R1 844

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
319 439 0.964358 GGCAGCTCAGAGCATTGGTT 60.964 55.0 24.64 0.0 45.56 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 3400 0.324943 ATCCACCCGAAAGTGACCAG 59.675 55.0 2.28 0.0 40.34 4.0 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.306917 TTGGTGTAATCGTGACGATGT 57.693 42.857 22.11 13.50 46.30 3.06
21 22 3.306917 TGGTGTAATCGTGACGATGTT 57.693 42.857 22.11 10.17 46.30 2.71
22 23 3.247442 TGGTGTAATCGTGACGATGTTC 58.753 45.455 22.11 14.38 46.30 3.18
23 24 2.278094 GGTGTAATCGTGACGATGTTCG 59.722 50.000 22.11 0.00 46.30 3.95
24 25 1.915350 TGTAATCGTGACGATGTTCGC 59.085 47.619 22.11 10.25 46.30 4.70
25 26 1.915350 GTAATCGTGACGATGTTCGCA 59.085 47.619 22.11 0.25 46.30 5.10
26 27 1.640428 AATCGTGACGATGTTCGCAT 58.360 45.000 22.11 0.20 46.30 4.73
27 28 1.200483 ATCGTGACGATGTTCGCATC 58.800 50.000 20.73 0.00 45.24 3.91
35 36 3.812577 ATGTTCGCATCACTCACGA 57.187 47.368 0.00 0.00 30.78 4.35
36 37 2.078849 ATGTTCGCATCACTCACGAA 57.921 45.000 0.00 0.00 42.95 3.85
37 38 2.078849 TGTTCGCATCACTCACGAAT 57.921 45.000 0.11 0.00 46.20 3.34
38 39 1.992667 TGTTCGCATCACTCACGAATC 59.007 47.619 0.11 0.00 46.20 2.52
39 40 2.263077 GTTCGCATCACTCACGAATCT 58.737 47.619 0.11 0.00 46.20 2.40
40 41 2.654749 TCGCATCACTCACGAATCTT 57.345 45.000 0.00 0.00 31.97 2.40
41 42 2.262211 TCGCATCACTCACGAATCTTG 58.738 47.619 0.00 0.00 31.97 3.02
42 43 1.995484 CGCATCACTCACGAATCTTGT 59.005 47.619 0.00 0.00 0.00 3.16
43 44 3.119637 TCGCATCACTCACGAATCTTGTA 60.120 43.478 0.00 0.00 31.97 2.41
44 45 3.612423 CGCATCACTCACGAATCTTGTAA 59.388 43.478 0.00 0.00 0.00 2.41
45 46 4.091365 CGCATCACTCACGAATCTTGTAAA 59.909 41.667 0.00 0.00 0.00 2.01
46 47 5.389411 CGCATCACTCACGAATCTTGTAAAA 60.389 40.000 0.00 0.00 0.00 1.52
47 48 6.370593 GCATCACTCACGAATCTTGTAAAAA 58.629 36.000 0.00 0.00 0.00 1.94
48 49 6.303259 GCATCACTCACGAATCTTGTAAAAAC 59.697 38.462 0.00 0.00 0.00 2.43
49 50 7.576236 CATCACTCACGAATCTTGTAAAAACT 58.424 34.615 0.00 0.00 0.00 2.66
50 51 6.943981 TCACTCACGAATCTTGTAAAAACTG 58.056 36.000 0.00 0.00 0.00 3.16
51 52 6.759356 TCACTCACGAATCTTGTAAAAACTGA 59.241 34.615 0.00 0.00 0.00 3.41
52 53 7.441157 TCACTCACGAATCTTGTAAAAACTGAT 59.559 33.333 0.00 0.00 0.00 2.90
53 54 8.070171 CACTCACGAATCTTGTAAAAACTGATT 58.930 33.333 0.00 0.00 0.00 2.57
54 55 8.283291 ACTCACGAATCTTGTAAAAACTGATTC 58.717 33.333 0.00 0.00 39.43 2.52
55 56 8.378172 TCACGAATCTTGTAAAAACTGATTCT 57.622 30.769 0.00 0.00 40.17 2.40
56 57 8.495949 TCACGAATCTTGTAAAAACTGATTCTC 58.504 33.333 0.00 0.00 40.17 2.87
57 58 8.499162 CACGAATCTTGTAAAAACTGATTCTCT 58.501 33.333 0.00 0.00 40.17 3.10
58 59 8.713271 ACGAATCTTGTAAAAACTGATTCTCTC 58.287 33.333 0.00 0.00 40.17 3.20
59 60 8.930760 CGAATCTTGTAAAAACTGATTCTCTCT 58.069 33.333 0.00 0.00 40.17 3.10
79 80 9.909644 TCTCTCTTCTATAAAAATATGGTACGC 57.090 33.333 0.00 0.00 0.00 4.42
80 81 9.692749 CTCTCTTCTATAAAAATATGGTACGCA 57.307 33.333 0.00 0.00 0.00 5.24
139 140 2.880890 TGCAAGCTCTCTTCAAAACCTC 59.119 45.455 0.00 0.00 0.00 3.85
150 151 5.547465 TCTTCAAAACCTCTATTCGCTCAA 58.453 37.500 0.00 0.00 0.00 3.02
152 153 4.000988 TCAAAACCTCTATTCGCTCAACC 58.999 43.478 0.00 0.00 0.00 3.77
161 162 4.825085 TCTATTCGCTCAACCAAAAGGTTT 59.175 37.500 0.00 0.00 0.00 3.27
319 439 0.964358 GGCAGCTCAGAGCATTGGTT 60.964 55.000 24.64 0.00 45.56 3.67
324 444 1.404391 GCTCAGAGCATTGGTTGATGG 59.596 52.381 18.17 0.00 41.89 3.51
418 538 1.153939 ACAGCTCATCACGTCTCGC 60.154 57.895 0.00 0.00 0.00 5.03
449 575 3.302347 AAGGCCGCTTGAGTCCTCG 62.302 63.158 0.00 0.00 0.00 4.63
453 579 1.004918 CCGCTTGAGTCCTCGGTTT 60.005 57.895 6.64 0.00 37.33 3.27
467 593 9.807649 GAGTCCTCGGTTTTGTATATAACTTAA 57.192 33.333 0.00 0.00 0.00 1.85
482 608 4.868314 AACTTAAACGAGTAGTCCAGCT 57.132 40.909 0.00 0.00 0.00 4.24
739 878 5.763204 CCAACTTTAGTTTGCCTGAAGTCTA 59.237 40.000 0.76 0.00 46.15 2.59
801 950 4.157105 CGGTACCGGATTGGAAGAAAAATT 59.843 41.667 27.00 0.00 42.00 1.82
802 951 5.407502 GGTACCGGATTGGAAGAAAAATTG 58.592 41.667 9.46 0.00 42.00 2.32
803 952 4.535526 ACCGGATTGGAAGAAAAATTGG 57.464 40.909 9.46 0.00 42.00 3.16
804 953 4.156477 ACCGGATTGGAAGAAAAATTGGA 58.844 39.130 9.46 0.00 42.00 3.53
805 954 4.591072 ACCGGATTGGAAGAAAAATTGGAA 59.409 37.500 9.46 0.00 42.00 3.53
806 955 5.170748 CCGGATTGGAAGAAAAATTGGAAG 58.829 41.667 0.00 0.00 42.00 3.46
807 956 5.047377 CCGGATTGGAAGAAAAATTGGAAGA 60.047 40.000 0.00 0.00 42.00 2.87
808 957 6.454795 CGGATTGGAAGAAAAATTGGAAGAA 58.545 36.000 0.00 0.00 0.00 2.52
933 1850 5.045724 TGGCCATAATCATTCCTTTTTGCTT 60.046 36.000 0.00 0.00 0.00 3.91
987 1905 3.181501 CCGAGTTTTCAAGAAACAGCACA 60.182 43.478 4.68 0.00 32.81 4.57
1108 2030 4.745783 GCAACTAACTAAGGTTGTGGAGGT 60.746 45.833 0.00 0.00 43.07 3.85
1333 2290 1.783031 GCTGCCTCATCCATGCTTCG 61.783 60.000 0.00 0.00 0.00 3.79
1342 2299 2.124819 CATGCTTCGAGGGCTGCT 60.125 61.111 12.40 0.00 0.00 4.24
1368 2325 0.906775 TTCCCACCTGGTAATCGTCC 59.093 55.000 0.00 0.00 34.77 4.79
1403 2494 4.834453 CGAGGGAGCAGCTGCAGG 62.834 72.222 38.24 17.18 45.16 4.85
1412 2503 2.036414 AGCTGCAGGAGACCGAGA 59.964 61.111 17.12 0.00 0.00 4.04
1422 2513 1.475403 GAGACCGAGACAATCCCAGA 58.525 55.000 0.00 0.00 0.00 3.86
1461 2552 7.935755 AGATGGTCAGGTGATGATAGTATTTTG 59.064 37.037 0.00 0.00 40.92 2.44
1490 2581 5.073311 TGTGTTCATCCAAGTAGCTAGTC 57.927 43.478 0.44 0.00 0.00 2.59
1512 2603 3.246226 CGCAGTTTCAGACCATACTATGC 59.754 47.826 0.00 0.00 0.00 3.14
1562 2654 1.979809 TTGGTATGATCACCCCAGGT 58.020 50.000 13.33 0.00 37.84 4.00
1623 2718 2.371179 GAGGATGGAGATGGAGATGCAA 59.629 50.000 0.00 0.00 0.00 4.08
1760 2855 6.183360 ACAGTTGTGTATGTTTCTCAAACTGG 60.183 38.462 14.56 0.64 37.43 4.00
1802 2933 7.204243 AGGGCATGAAGAGCATCATATATAA 57.796 36.000 0.00 0.00 37.96 0.98
1843 2997 5.835113 AGCGCCATTTTATATTTGTGAGT 57.165 34.783 2.29 0.00 0.00 3.41
1910 3070 3.836562 AGAAGCCAGCCAAAAATCTCAAT 59.163 39.130 0.00 0.00 0.00 2.57
1929 3089 3.764885 ATGGCTGATTTCGTAAAGTGC 57.235 42.857 0.00 0.00 0.00 4.40
2040 3202 8.229253 TGCACTTAAGCTATGATTTCATCAAT 57.771 30.769 1.29 0.00 37.91 2.57
2069 3260 2.200370 ACACCACGGGAGAGACCA 59.800 61.111 0.00 0.00 41.20 4.02
2073 3264 0.252284 ACCACGGGAGAGACCAAGAT 60.252 55.000 0.00 0.00 41.20 2.40
2180 3400 6.426937 TGAGTGACAACTAAGAAACCATTAGC 59.573 38.462 0.00 0.00 36.52 3.09
2268 3488 6.515832 CATGAGCTGTATGGTATTGTCACTA 58.484 40.000 0.00 0.00 0.00 2.74
2350 3570 4.713792 AAGGATGGAAAAGTGTGAGAGT 57.286 40.909 0.00 0.00 0.00 3.24
2387 3607 1.098050 GTACTTTCCGTCGGCCTAGA 58.902 55.000 6.34 0.00 0.00 2.43
2388 3608 1.065251 GTACTTTCCGTCGGCCTAGAG 59.935 57.143 6.34 0.00 0.00 2.43
2487 4704 2.459555 ATATGCTTGTTTGGAGGGGG 57.540 50.000 0.00 0.00 0.00 5.40
2517 4734 4.388577 AAAAGTGTCCAATCTAAGCCCT 57.611 40.909 0.00 0.00 0.00 5.19
2576 4850 8.787852 AGAAGTGTTTTGACTAGAATTTGGATC 58.212 33.333 0.00 0.00 0.00 3.36
2586 4860 6.574350 ACTAGAATTTGGATCGTGAGTAAGG 58.426 40.000 0.00 0.00 0.00 2.69
2594 4868 3.305813 GGATCGTGAGTAAGGACACACAA 60.306 47.826 6.49 0.00 44.65 3.33
2595 4869 3.364889 TCGTGAGTAAGGACACACAAG 57.635 47.619 6.49 0.00 44.65 3.16
2596 4870 1.792949 CGTGAGTAAGGACACACAAGC 59.207 52.381 6.49 0.00 44.65 4.01
2629 4905 4.633175 GCTAGAGTTATACCTGCTTTCCC 58.367 47.826 0.00 0.00 0.00 3.97
2657 4933 4.671377 TCATTGAAACAAAGAGTGCACAC 58.329 39.130 21.04 13.64 0.00 3.82
2659 4935 4.717233 TTGAAACAAAGAGTGCACACAT 57.283 36.364 21.04 2.17 0.00 3.21
2670 4946 1.750778 GTGCACACATAAGATTGGGGG 59.249 52.381 13.17 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.306917 ACATCGTCACGATTACACCAA 57.693 42.857 10.81 0.00 44.59 3.67
1 2 3.247442 GAACATCGTCACGATTACACCA 58.753 45.455 10.81 0.00 44.59 4.17
2 3 2.278094 CGAACATCGTCACGATTACACC 59.722 50.000 10.81 0.00 44.59 4.16
3 4 2.284288 GCGAACATCGTCACGATTACAC 60.284 50.000 10.81 1.85 44.59 2.90
4 5 1.915350 GCGAACATCGTCACGATTACA 59.085 47.619 10.81 0.00 44.59 2.41
5 6 1.915350 TGCGAACATCGTCACGATTAC 59.085 47.619 10.81 4.04 44.59 1.89
6 7 2.265647 TGCGAACATCGTCACGATTA 57.734 45.000 10.81 0.00 44.59 1.75
7 8 1.588404 GATGCGAACATCGTCACGATT 59.412 47.619 10.81 0.00 44.59 3.34
9 10 2.648972 GATGCGAACATCGTCACGA 58.351 52.632 0.28 0.28 43.15 4.35
17 18 2.078849 TTCGTGAGTGATGCGAACAT 57.921 45.000 0.00 0.00 39.30 2.71
18 19 1.992667 GATTCGTGAGTGATGCGAACA 59.007 47.619 0.00 0.00 45.36 3.18
19 20 2.263077 AGATTCGTGAGTGATGCGAAC 58.737 47.619 0.00 0.00 45.36 3.95
20 21 2.654749 AGATTCGTGAGTGATGCGAA 57.345 45.000 0.00 0.00 46.33 4.70
21 22 2.262211 CAAGATTCGTGAGTGATGCGA 58.738 47.619 0.00 0.00 0.00 5.10
22 23 1.995484 ACAAGATTCGTGAGTGATGCG 59.005 47.619 6.60 0.00 0.00 4.73
23 24 5.530519 TTTACAAGATTCGTGAGTGATGC 57.469 39.130 6.60 0.00 0.00 3.91
24 25 7.531871 CAGTTTTTACAAGATTCGTGAGTGATG 59.468 37.037 6.60 0.00 0.00 3.07
25 26 7.441157 TCAGTTTTTACAAGATTCGTGAGTGAT 59.559 33.333 6.60 0.00 0.00 3.06
26 27 6.759356 TCAGTTTTTACAAGATTCGTGAGTGA 59.241 34.615 6.60 0.15 0.00 3.41
27 28 6.943981 TCAGTTTTTACAAGATTCGTGAGTG 58.056 36.000 6.60 0.00 0.00 3.51
28 29 7.730364 ATCAGTTTTTACAAGATTCGTGAGT 57.270 32.000 6.60 0.00 0.00 3.41
29 30 8.499162 AGAATCAGTTTTTACAAGATTCGTGAG 58.501 33.333 6.60 0.00 45.56 3.51
30 31 8.378172 AGAATCAGTTTTTACAAGATTCGTGA 57.622 30.769 6.60 0.00 45.56 4.35
31 32 8.499162 AGAGAATCAGTTTTTACAAGATTCGTG 58.501 33.333 0.00 0.00 45.56 4.35
32 33 8.608844 AGAGAATCAGTTTTTACAAGATTCGT 57.391 30.769 0.00 0.00 45.56 3.85
33 34 8.930760 AGAGAGAATCAGTTTTTACAAGATTCG 58.069 33.333 0.00 0.00 45.56 3.34
53 54 9.909644 GCGTACCATATTTTTATAGAAGAGAGA 57.090 33.333 0.00 0.00 0.00 3.10
54 55 9.692749 TGCGTACCATATTTTTATAGAAGAGAG 57.307 33.333 0.00 0.00 0.00 3.20
101 102 4.460731 GCTTGCAGAGTAAGGGATCTTTTT 59.539 41.667 0.00 0.00 34.59 1.94
102 103 4.013050 GCTTGCAGAGTAAGGGATCTTTT 58.987 43.478 0.00 0.00 34.59 2.27
103 104 3.265479 AGCTTGCAGAGTAAGGGATCTTT 59.735 43.478 0.00 0.00 34.59 2.52
104 105 2.843113 AGCTTGCAGAGTAAGGGATCTT 59.157 45.455 0.00 0.00 37.03 2.40
364 484 3.012274 AGAACTTCCAGATCTCCCTCTCA 59.988 47.826 0.00 0.00 0.00 3.27
467 593 4.017808 AGACATTAGCTGGACTACTCGTT 58.982 43.478 0.00 0.00 0.00 3.85
479 605 2.185004 AACAACGCCAGACATTAGCT 57.815 45.000 0.00 0.00 0.00 3.32
482 608 2.697431 GCAAACAACGCCAGACATTA 57.303 45.000 0.00 0.00 0.00 1.90
728 867 1.271379 TGTGGGCTTTAGACTTCAGGC 60.271 52.381 0.00 0.00 0.00 4.85
801 950 9.701098 CAAATGATTCTGAAGATTTTTCTTCCA 57.299 29.630 11.96 4.36 43.94 3.53
802 951 8.654215 GCAAATGATTCTGAAGATTTTTCTTCC 58.346 33.333 11.96 0.00 43.94 3.46
803 952 9.199982 TGCAAATGATTCTGAAGATTTTTCTTC 57.800 29.630 8.45 8.45 44.60 2.87
804 953 8.985805 GTGCAAATGATTCTGAAGATTTTTCTT 58.014 29.630 0.00 0.00 0.00 2.52
805 954 7.601508 GGTGCAAATGATTCTGAAGATTTTTCT 59.398 33.333 0.00 0.00 0.00 2.52
806 955 7.385752 TGGTGCAAATGATTCTGAAGATTTTTC 59.614 33.333 0.00 4.71 0.00 2.29
807 956 7.218614 TGGTGCAAATGATTCTGAAGATTTTT 58.781 30.769 0.00 0.00 0.00 1.94
808 957 6.761312 TGGTGCAAATGATTCTGAAGATTTT 58.239 32.000 0.00 0.06 0.00 1.82
867 1036 8.262933 GGGTATAAGTAAAGCAGAAAGTTAGGA 58.737 37.037 0.00 0.00 0.00 2.94
933 1850 4.947147 AGCACGCGAAAAGGGGCA 62.947 61.111 15.93 0.00 37.07 5.36
987 1905 2.213499 GCTAGCATTTCGTAGGCATGT 58.787 47.619 10.63 0.00 0.00 3.21
1108 2030 1.632409 AGATTGAGGCCTCTGAAGCAA 59.368 47.619 32.28 18.58 0.00 3.91
1300 2257 2.818714 CAGCAGAAGCCGAGCAGG 60.819 66.667 0.00 0.00 43.56 4.85
1333 2290 2.234143 GGGAATGAAATAGCAGCCCTC 58.766 52.381 0.00 0.00 34.94 4.30
1403 2494 1.475403 TCTGGGATTGTCTCGGTCTC 58.525 55.000 0.00 0.00 0.00 3.36
1412 2503 2.240667 CTCCACTGGAATCTGGGATTGT 59.759 50.000 0.00 0.00 0.00 2.71
1422 2513 1.211457 GACCATCTGCTCCACTGGAAT 59.789 52.381 0.00 0.00 32.92 3.01
1461 2552 5.449177 GCTACTTGGATGAACACAAATAGCC 60.449 44.000 6.61 0.00 43.00 3.93
1490 2581 3.246226 GCATAGTATGGTCTGAAACTGCG 59.754 47.826 12.07 0.00 0.00 5.18
1512 2603 2.610232 GCCAATTACAGTTTGCACCTGG 60.610 50.000 15.10 0.00 34.16 4.45
1562 2654 2.513204 CCTCTCCCGCTACGACGA 60.513 66.667 0.00 0.00 34.06 4.20
1601 2696 2.259012 GCATCTCCATCTCCATCCTCT 58.741 52.381 0.00 0.00 0.00 3.69
1623 2718 2.363361 CCCGGGTAGTCCTCCAGT 59.637 66.667 14.18 0.00 0.00 4.00
1760 2855 2.604614 CCCTTGCAAGTAACAAGCGTTC 60.605 50.000 24.35 0.00 42.57 3.95
1802 2933 2.349532 GCTTTTCGTCGCTAGTGCTTTT 60.350 45.455 0.00 0.00 36.97 2.27
1910 3070 1.810151 GGCACTTTACGAAATCAGCCA 59.190 47.619 0.00 0.00 40.50 4.75
1929 3089 4.932200 GTCTATAAATTCTGGATCCAGCGG 59.068 45.833 33.39 14.66 43.31 5.52
2040 3202 3.055021 TCCCGTGGTGTGCTATCAAATTA 60.055 43.478 0.00 0.00 0.00 1.40
2180 3400 0.324943 ATCCACCCGAAAGTGACCAG 59.675 55.000 2.28 0.00 40.34 4.00
2224 3444 2.294233 TGCAGTTTTCAGCACCATCTTC 59.706 45.455 0.00 0.00 37.41 2.87
2268 3488 7.759489 TTACCTTGCATGATCAAGTAAAACT 57.241 32.000 0.00 0.00 41.29 2.66
2350 3570 7.227910 GGAAAGTACGCAAATTCCTAATATGGA 59.772 37.037 8.97 0.00 38.61 3.41
2387 3607 5.928839 GCATGATATTGAATACACCGTCTCT 59.071 40.000 0.00 0.00 0.00 3.10
2388 3608 5.928839 AGCATGATATTGAATACACCGTCTC 59.071 40.000 0.00 0.00 0.00 3.36
2487 4704 8.718102 TTAGATTGGACACTTTTAGACTATGC 57.282 34.615 0.00 0.00 0.00 3.14
2555 4772 6.708502 TCACGATCCAAATTCTAGTCAAAACA 59.291 34.615 0.00 0.00 0.00 2.83
2564 4838 6.153851 TGTCCTTACTCACGATCCAAATTCTA 59.846 38.462 0.00 0.00 0.00 2.10
2586 4860 3.182967 CGAATCTCTAGGCTTGTGTGTC 58.817 50.000 0.00 0.00 0.00 3.67
2594 4868 3.502123 ACTCTAGCGAATCTCTAGGCT 57.498 47.619 7.35 0.00 39.44 4.58
2595 4869 5.890424 ATAACTCTAGCGAATCTCTAGGC 57.110 43.478 7.35 0.00 35.43 3.93
2596 4870 7.065324 CAGGTATAACTCTAGCGAATCTCTAGG 59.935 44.444 7.35 1.92 35.43 3.02
2629 4905 5.200454 CACTCTTTGTTTCAATGAGTCACG 58.800 41.667 20.29 11.21 36.05 4.35
2657 4933 6.320164 TCAACGTAATTTCCCCCAATCTTATG 59.680 38.462 0.00 0.00 0.00 1.90
2659 4935 5.817784 TCAACGTAATTTCCCCCAATCTTA 58.182 37.500 0.00 0.00 0.00 2.10


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.